Factors affecting synonymous codon usage of housekeeping genes in Drosophila melanogaster

Housekeeping genes (HK genes) are required for cell survival and the maintenance of basic cellular functions. The investigation of factors affecting codon usage patterns in HK genes of insects can help in understanding the molecular evolution of insects and aid the development of insect pest management strategies. In this study, we employed bioinformatics approaches to analyze the codon usage bias (CUB) of HK genes in the insect model organism, Drosophila melanogaster. A comparison of CUB between 1107 HK genes and 1084 high tissue specificity genes suggested that HK genes have higher CUB in D. melanogaster. In addition, we found that CUB inversely correlates with the non-synonymous substitution rate of HK genes. Therefore, we attempted to identify the factors that potentially influence the codon usage pattern of HK genes. Our results suggest that mutation pressure and natural selection highly correlate with CUB in the HK genes of D. melanogaster and that two topological properties of HK proteins (proportion of protein interacting length and protein connectivity) also correlate with CUB in the HK genes of D. melanogaster. This study provides insight into CUB in the HK genes of D. melanogaster, and the results can support future investigations of potential applications in agricultural and biomedical field.